Indrek Kalvet

De novo design and evolution of an artificial metathase for cytoplasmic olefin metathesis Nature Catalysis, Published online: 03 November 2025; doi:10.1038/s41929-025-01436-0The creation of artificial metalloenzymes compatible with complex biological settings could enable broad applications. Now a de novo-designed artificial metalloenzyme containing an abiological ruthenium cofactor is reported and optimized for ring-closing metathesis in the cytoplasm of whole cells.

New online! De novo design and evolution of an artificial metathase for cytoplasmic olefin metathesis

(oops, that is supposed to be a GIF, but it doesn't work on bsky...)

RFdiffusion2 is now live!
github.com/RosettaCommo...

You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!

Computational design of serine hydrolases The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of ...

PLACER played a valuable role in helping my colleagues Anna and @spellock.bsky.social design novel serine hydrolases from scratch:
www.science.org/doi/10.1126/...

GitHub - baker-laboratory/PLACER: PLACER is graph neural network for local prediction of protein-ligand conformational ensembles. PLACER is graph neural network for local prediction of protein-ligand conformational ensembles. - baker-laboratory/PLACER

We are happy to share that the code and weights of PLACER (formerly known as ChemNet) are now public!
This method allows for rapid evaluation of protein side chain and ligand conformational ensembles, with uses in ligand docking and enzyme evaluation.
github.com/baker-labora...